Undernutrition and diarrhoeal disease are major causes of infant mortality. We investigated the combined roles of breastfeeding and diarrhoea on infant size in 2940 infants from the Cebu Longitudinal Health and Nutrition Survey. The study aimed to assess whether breastfeeding status modified the deficits associated with diarrhoeal disease. The primary exposures were combinations of current breastfeeding status (yes/no), the presence of diarrhoeal disease in previous week (yes/no) and a categorical survey variable (six surveys taken at bimonthly intervals when infants were 2–12 months of age). Relative weight (weight-for-length z-scores), calculated using the WHO growth standards, was estimated using sex-stratified, fixed-effects longitudinal models that also adjusted for energy from complementary foods. Post-estimation Wald tests were conducted to identify subgroup differences in relative weight. Diarrhoea was associated with reduced relative weight in both breastfed and non-breastfed infants of 6–12 months. Diarrhoea-related deficits in relative weight were significantly exacerbated in non-breastfed girls of 6 and 8 months. Importantly, in infants <6 months, being breastfed and having diarrhoea was still associated with greater relative weight compared with being non-breastfed and diarrhoea-free. Breastfeeding emerged as a strong contributor to relative weight in younger infants (<6 months) while diarrhoeal disease strongly contributed to deficits in relative weight in older infants (6–12 months). These findings underscore the importance of breastfeeding for promoting infant nutritional status in infants with or without diarrhoea from birth to 12 months.